A segmentation-and-spectrum-based metal artifact reduction (MAR) system and method is applied in polychromatic X-ray CT system that uses a priori knowledge of high-Z metals in samples which contribute the primary artifacts at a known x-ray energy spectrum. Using a basis materials decomposition, the method solves the problem of reducing or eliminating metal artifacts associated with beam hardening using only a single scan of the sample performed at selected x-ray energy.